use a 3rd party partition softwarem to merge the two partition, but if your Windows OS is windows7/8, I think you mean the two partition are "System Reserved E:" and "System C:" partition, that two partitions can not be merged by partition software you need to do series of configuration to remove System reserved partition, you can ask Google for help about remove recovery partition.
Here are my ways for you to emerge your partitions:
1. Back up your important data well in case of any data loss in the following operation.
2. Right click “My Computer” to select “Manage”
3. Double click “Disk Management”.
4. Right click the volume that you wan to delete and hit “Delete Volume”.
5. Right click the volume that you want to expand and select “Extend Volume”. Afterwards, your computer will automatically emerge them for you.